[Chimera-users] dotted lines

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 15 15:36:30 PST 2015


Hi Thomas,
Sure!  The line style and line width are attributes of a pseudobond group (for example, all distance measurements), so you can only change them for the whole group at once.

(1) One way is to use the Selection Inspector:  select any distance line with  Ctrl-click, then click the green magnifying glass icon near the bottom corner of the Chimera window to open the Selection Inspector.  In the Inspector, inspect "Pseudobond Group" (not Pseudobond!) to change line style and/or line width.   If you put the cursor over an entry in the dialog, it will show  balloon help with the attribute name, which you would need if you wanted to use commands instead of the dialog.  For example, this tells me that "line style" is the attribute "lineType" with values 1=solid, 2=dashed, 3=dotted, 4=dash-dot, 5=dash-dot-dot.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

(2) So, a second way is to use the "setattr" command.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

For example:

setattr g lineType 2
setattr g lineWidth 3

… would change ALL pseudobonds (distances but also any others like metal complex bonds) to dashed with line width 3.  To change only specific pseudobond groups, you'd need to end with an atom-spec that includes both ends of least one pseudobond in that group, e.g. something like:

setattr g lineType  4  :44,47

… to make all distance pseudobonds dash-dot (assuming at least one distance measurement is between residues 44 and 47). 

(3) For distance measurements specifically, you can set how you want them to look when first created. To do that, show the Distances tool (in menu under Tools… Structure Analysis), then set the "Depiction options" on the right side of the dialog before adding the distance measurement.  You can click Save to make these depiction settings apply to later uses of Chimera as well.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 15, 2015, at 3:06 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:

> Greetings,
> I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed?
> thanks,
> Thomas
> 




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